Job ID = 5721197 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-04-15T20:45:22 fasterq-dump.2.9.6 sys: timeout exhausted while reading file within network system module - mbedtls_ssl_read returned -76 ( NET - Reading information from the socket failed ) 2020-04-15T20:45:22 fasterq-dump.2.9.6 sys: timeout exhausted while reading file within network system module - mbedtls_ssl_read returned -76 ( NET - Reading information from the socket failed ) 2020-04-15T20:46:24 fasterq-dump.2.9.6 sys: error unknown while reading file within network system module - mbedtls_ssl_read returned -76 ( NET - Reading information from the socket failed ) spots read : 25,845,210 reads read : 25,845,210 reads written : 25,845,210 rm: cannot remove ‘[DSE]RR*’: No such file or directory fastq に変換しました。 bowtie でマッピング中... Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:09:55 25845210 reads; of these: 25845210 (100.00%) were unpaired; of these: 797649 (3.09%) aligned 0 times 16702315 (64.62%) aligned exactly 1 time 8345246 (32.29%) aligned >1 times 96.91% overall alignment rate Time searching: 00:09:55 Overall time: 00:09:55 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 15 sequences. [bam_sort_core] merging from 12 files... [bam_rmdupse_core] 4286623 / 25047561 = 0.1711 in library ' ' BAM に変換しました。 Bed ファイルを作成中... WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Thu, 16 Apr 2020 06:09:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6827665/SRX6827665.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6827665/SRX6827665.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6827665/SRX6827665.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6827665/SRX6827665.bam'] # control file = None # effective genome size = 1.20e+08 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-05 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Thu, 16 Apr 2020 06:09:31: #1 read tag files... INFO @ Thu, 16 Apr 2020 06:09:31: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 06:09:37: 1000000 INFO @ Thu, 16 Apr 2020 06:09:43: 2000000 INFO @ Thu, 16 Apr 2020 06:09:49: 3000000 INFO @ Thu, 16 Apr 2020 06:09:55: 4000000 WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Thu, 16 Apr 2020 06:10:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6827665/SRX6827665.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6827665/SRX6827665.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6827665/SRX6827665.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6827665/SRX6827665.bam'] # control file = None # effective genome size = 1.20e+08 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-10 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Thu, 16 Apr 2020 06:10:01: #1 read tag files... INFO @ Thu, 16 Apr 2020 06:10:01: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 06:10:01: 5000000 INFO @ Thu, 16 Apr 2020 06:10:07: 1000000 INFO @ Thu, 16 Apr 2020 06:10:08: 6000000 INFO @ Thu, 16 Apr 2020 06:10:14: 2000000 INFO @ Thu, 16 Apr 2020 06:10:14: 7000000 INFO @ Thu, 16 Apr 2020 06:10:20: 3000000 INFO @ Thu, 16 Apr 2020 06:10:21: 8000000 INFO @ Thu, 16 Apr 2020 06:10:27: 4000000 INFO @ Thu, 16 Apr 2020 06:10:28: 9000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Thu, 16 Apr 2020 06:10:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6827665/SRX6827665.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6827665/SRX6827665.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6827665/SRX6827665.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6827665/SRX6827665.bam'] # control file = None # effective genome size = 1.20e+08 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-20 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Thu, 16 Apr 2020 06:10:31: #1 read tag files... INFO @ Thu, 16 Apr 2020 06:10:31: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 06:10:33: 5000000 INFO @ Thu, 16 Apr 2020 06:10:35: 10000000 INFO @ Thu, 16 Apr 2020 06:10:39: 1000000 INFO @ Thu, 16 Apr 2020 06:10:41: 6000000 INFO @ Thu, 16 Apr 2020 06:10:42: 11000000 INFO @ Thu, 16 Apr 2020 06:10:47: 2000000 INFO @ Thu, 16 Apr 2020 06:10:48: 7000000 INFO @ Thu, 16 Apr 2020 06:10:50: 12000000 INFO @ Thu, 16 Apr 2020 06:10:55: 3000000 INFO @ Thu, 16 Apr 2020 06:10:56: 8000000 INFO @ Thu, 16 Apr 2020 06:10:57: 13000000 INFO @ Thu, 16 Apr 2020 06:11:03: 4000000 INFO @ Thu, 16 Apr 2020 06:11:03: 9000000 INFO @ Thu, 16 Apr 2020 06:11:04: 14000000 INFO @ Thu, 16 Apr 2020 06:11:11: 10000000 INFO @ Thu, 16 Apr 2020 06:11:11: 5000000 INFO @ Thu, 16 Apr 2020 06:11:12: 15000000 INFO @ Thu, 16 Apr 2020 06:11:18: 11000000 INFO @ Thu, 16 Apr 2020 06:11:19: 6000000 INFO @ Thu, 16 Apr 2020 06:11:19: 16000000 INFO @ Thu, 16 Apr 2020 06:11:25: 12000000 INFO @ Thu, 16 Apr 2020 06:11:27: 17000000 INFO @ Thu, 16 Apr 2020 06:11:28: 7000000 INFO @ Thu, 16 Apr 2020 06:11:33: 13000000 INFO @ Thu, 16 Apr 2020 06:11:34: 18000000 INFO @ Thu, 16 Apr 2020 06:11:36: 8000000 INFO @ Thu, 16 Apr 2020 06:11:40: 14000000 INFO @ Thu, 16 Apr 2020 06:11:42: 19000000 INFO @ Thu, 16 Apr 2020 06:11:44: 9000000 INFO @ Thu, 16 Apr 2020 06:11:47: 15000000 INFO @ Thu, 16 Apr 2020 06:11:49: 20000000 INFO @ Thu, 16 Apr 2020 06:11:52: 10000000 INFO @ Thu, 16 Apr 2020 06:11:55: 16000000 INFO @ Thu, 16 Apr 2020 06:11:55: #1 tag size is determined as 50 bps INFO @ Thu, 16 Apr 2020 06:11:55: #1 tag size = 50 INFO @ Thu, 16 Apr 2020 06:11:55: #1 total tags in treatment: 20760938 INFO @ Thu, 16 Apr 2020 06:11:55: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 06:11:55: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 16 Apr 2020 06:11:55: #1 tags after filtering in treatment: 20760938 INFO @ Thu, 16 Apr 2020 06:11:55: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 06:11:55: #1 finished! INFO @ Thu, 16 Apr 2020 06:11:55: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 06:11:55: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 06:11:57: #2 number of paired peaks: 463 WARNING @ Thu, 16 Apr 2020 06:11:57: Fewer paired peaks (463) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 463 pairs to build model! INFO @ Thu, 16 Apr 2020 06:11:57: start model_add_line... INFO @ Thu, 16 Apr 2020 06:11:57: start X-correlation... INFO @ Thu, 16 Apr 2020 06:11:57: end of X-cor INFO @ Thu, 16 Apr 2020 06:11:57: #2 finished! INFO @ Thu, 16 Apr 2020 06:11:57: #2 predicted fragment length is 50 bps INFO @ Thu, 16 Apr 2020 06:11:57: #2 alternative fragment length(s) may be 4,50 bps INFO @ Thu, 16 Apr 2020 06:11:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6827665/SRX6827665.05_model.r WARNING @ Thu, 16 Apr 2020 06:11:57: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 06:11:57: #2 You may need to consider one of the other alternative d(s): 4,50 WARNING @ Thu, 16 Apr 2020 06:11:57: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 16 Apr 2020 06:11:57: #3 Call peaks... INFO @ Thu, 16 Apr 2020 06:11:57: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 06:12:00: 11000000 INFO @ Thu, 16 Apr 2020 06:12:02: 17000000 INFO @ Thu, 16 Apr 2020 06:12:08: 12000000 INFO @ Thu, 16 Apr 2020 06:12:10: 18000000 INFO @ Thu, 16 Apr 2020 06:12:16: 13000000 INFO @ Thu, 16 Apr 2020 06:12:17: 19000000 INFO @ Thu, 16 Apr 2020 06:12:24: 14000000 INFO @ Thu, 16 Apr 2020 06:12:24: 20000000 INFO @ Thu, 16 Apr 2020 06:12:30: #1 tag size is determined as 50 bps INFO @ Thu, 16 Apr 2020 06:12:30: #1 tag size = 50 INFO @ Thu, 16 Apr 2020 06:12:30: #1 total tags in treatment: 20760938 INFO @ Thu, 16 Apr 2020 06:12:30: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 06:12:30: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 16 Apr 2020 06:12:30: #1 tags after filtering in treatment: 20760938 INFO @ Thu, 16 Apr 2020 06:12:30: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 06:12:30: #1 finished! INFO @ Thu, 16 Apr 2020 06:12:30: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 06:12:30: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 06:12:32: #2 number of paired peaks: 463 WARNING @ Thu, 16 Apr 2020 06:12:32: Fewer paired peaks (463) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 463 pairs to build model! INFO @ Thu, 16 Apr 2020 06:12:32: start model_add_line... INFO @ Thu, 16 Apr 2020 06:12:32: start X-correlation... INFO @ Thu, 16 Apr 2020 06:12:32: end of X-cor INFO @ Thu, 16 Apr 2020 06:12:32: #2 finished! INFO @ Thu, 16 Apr 2020 06:12:32: #2 predicted fragment length is 50 bps INFO @ Thu, 16 Apr 2020 06:12:32: #2 alternative fragment length(s) may be 4,50 bps INFO @ Thu, 16 Apr 2020 06:12:32: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6827665/SRX6827665.10_model.r WARNING @ Thu, 16 Apr 2020 06:12:32: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 06:12:32: #2 You may need to consider one of the other alternative d(s): 4,50 WARNING @ Thu, 16 Apr 2020 06:12:32: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 16 Apr 2020 06:12:32: #3 Call peaks... INFO @ Thu, 16 Apr 2020 06:12:32: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 06:12:32: 15000000 INFO @ Thu, 16 Apr 2020 06:12:33: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 06:12:40: 16000000 INFO @ Thu, 16 Apr 2020 06:12:47: 17000000 INFO @ Thu, 16 Apr 2020 06:12:52: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6827665/SRX6827665.05_peaks.xls INFO @ Thu, 16 Apr 2020 06:12:52: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6827665/SRX6827665.05_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 06:12:52: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6827665/SRX6827665.05_summits.bed INFO @ Thu, 16 Apr 2020 06:12:52: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (3493 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 06:12:54: 18000000 INFO @ Thu, 16 Apr 2020 06:13:02: 19000000 INFO @ Thu, 16 Apr 2020 06:13:09: 20000000 INFO @ Thu, 16 Apr 2020 06:13:10: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 06:13:14: #1 tag size is determined as 50 bps INFO @ Thu, 16 Apr 2020 06:13:14: #1 tag size = 50 INFO @ Thu, 16 Apr 2020 06:13:14: #1 total tags in treatment: 20760938 INFO @ Thu, 16 Apr 2020 06:13:14: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 06:13:14: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 16 Apr 2020 06:13:15: #1 tags after filtering in treatment: 20760938 INFO @ Thu, 16 Apr 2020 06:13:15: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 06:13:15: #1 finished! INFO @ Thu, 16 Apr 2020 06:13:15: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 06:13:15: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 06:13:16: #2 number of paired peaks: 463 WARNING @ Thu, 16 Apr 2020 06:13:16: Fewer paired peaks (463) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 463 pairs to build model! INFO @ Thu, 16 Apr 2020 06:13:16: start model_add_line... INFO @ Thu, 16 Apr 2020 06:13:16: start X-correlation... INFO @ Thu, 16 Apr 2020 06:13:16: end of X-cor INFO @ Thu, 16 Apr 2020 06:13:16: #2 finished! INFO @ Thu, 16 Apr 2020 06:13:16: #2 predicted fragment length is 50 bps INFO @ Thu, 16 Apr 2020 06:13:16: #2 alternative fragment length(s) may be 4,50 bps INFO @ Thu, 16 Apr 2020 06:13:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6827665/SRX6827665.20_model.r WARNING @ Thu, 16 Apr 2020 06:13:16: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 06:13:16: #2 You may need to consider one of the other alternative d(s): 4,50 WARNING @ Thu, 16 Apr 2020 06:13:16: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 16 Apr 2020 06:13:16: #3 Call peaks... INFO @ Thu, 16 Apr 2020 06:13:16: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 06:13:28: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6827665/SRX6827665.10_peaks.xls INFO @ Thu, 16 Apr 2020 06:13:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6827665/SRX6827665.10_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 06:13:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6827665/SRX6827665.10_summits.bed INFO @ Thu, 16 Apr 2020 06:13:28: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (2530 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 06:13:53: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 06:14:12: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6827665/SRX6827665.20_peaks.xls INFO @ Thu, 16 Apr 2020 06:14:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6827665/SRX6827665.20_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 06:14:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6827665/SRX6827665.20_summits.bed INFO @ Thu, 16 Apr 2020 06:14:12: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (1397 records, 4 fields): 2 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。